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At least 829 records · Page 46
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Pressure-Induced Spectroscopic Changes in a Californium 1D Material Are Twice as Large as Found in the Holmium Analog

Here, in this study, the synthesis, characterization, and pressure response of a 1D californium mellitate (mellitate = 1,2,3,4,5,6-benzenehexacarboxylate) coordination polymer, Cf 2 (mell)(H 2 O) 10 ·4H 2 O (Cf-1), are reported. The Cf–O lengths within the crystal structure are compared to its gadolinium (Gd-1) and holmium (Ho-1) analogs as well. These data show that the average Cf–O bond distance is slightly longer than the average Gd–O bond, consistent with trends in effective ionic radii. UV–vis-NIR absorption spectra as a function of pressure were collected using diamond-anvil techniques for both Cf-1 and Ho-1. These experiments show that the Cf(III) f → f transitions have a stronger dependence on pressure than that of the holmium analog. In the former case, the shift is nearly linear with applied pressure and averages 6.6 cm –1 /GPa, whereas in the latter, it is <3 cm –1 /GPa.

absorption spectroscopy↗
DOE OSTI2022

Identification of Small-Molecule Inhibitors of Fibroblast Growth Factor 23 Signaling via In Silico Hot Spot Prediction and Molecular Docking to α-Klotho

Fibroblast growth factor 23 (FGF23) is a therapeutic target for treating hereditary and acquired hypophosphatemic disorders, such as X-linked hypophosphatemic (XLH) rickets and tumor-induced osteomalacia (TIO), respectively. FGF23-induced hypophosphatemia is mediated by signaling through a ternary complex formed by FGF23, the FGF receptor (FGFR), and α-Klotho. Currently, disorders of excess FGF23 are treated with an FGF23-blocking antibody, burosumab. Small-molecule drugs that disrupt protein/protein interactions necessary for the ternary complex formation offer an alternative to disrupting FGF23 signaling. In this study, the FGF23:α-Klotho interface was targeted to identify small-molecule protein/protein interaction inhibitors since it was computationally predicted to have a large fraction of hot spots and two druggable residues on α-Klotho. We further identified Tyr433 on the KL1 domain of α-Klotho as a promising hot spot and α-Klotho as an appropriate drug-binding target at this interface. Subsequently, we performed in silico docking of ~5.5 million compounds from the ZINC database to the interface region of α-Klotho from the ternary crystal structure. Following docking, 24 and 20 compounds were in the final list based on the lowest binding free energies to α-Klotho and the largest number of contacts with Tyr433, respectively. Herein, five compounds were assessed experimentally by their FGF23-mediated extracellular signal-regulated kinase (ERK) activities in vitro, and two of these reduced activities significantly. Both these compounds were predicted to have favorable binding affinities to α-Klotho but not have a large number of contacts with the hot spot Tyr433. ZINC12409120 was found experimentally to disrupt FGF23:α-Klotho interaction to reduce FGF23-mediated ERK activities by 70% and have a half maximal inhibitory concentration (IC50) of 5.0 ± 0.23 μM. Molecular dynamics (MD) simulations of the ZINC12409120:α-Klotho complex starting from in silico docking poses reveal that the ligand exhibits contacts with residues on the KL1 domain, the KL1–KL2 linker, and the KL2 domain of α-Klotho simultaneously, thereby possibly disrupting the regular function of α-Klotho and impeding FGF23:α-Klotho interaction. ZINC12409120 is a candidate for lead optimization.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Atomically thin interlayer phase from first principles enables defect-free incommensurate SnO2/CdTe interface

Advancing optoelectronic and emerging technologies increasingly requires control and design of interfaces between dissimilar materials. However, incommensurate interfaces are notoriously defective and rarely benefit from first-principles predictions, because no explicit atomic-structure models exist. Here, we adopt a bulk crystal structure prediction method to the interface geometry and apply it to SnO2/CdTe heterojunctions without and with the addition of CdCl2, a ubiquitous and beneficial, but abstruse processing step in CdTe photovoltaics. Whereas the direct SnO2/CdTe interface is highly defective, we discover a unique two-dimensional CdCl2 interphase, unrelated to the respective bulk structure. It facilitates a seamless transition from the rutile to zincblende lattices and removes defect-states from the interface bandgap. Implementing the predicted interface electronic structure in device simulations, we demonstrate the theoretical feasibility of bufferless oxide-CdTe heterojunction solar cells approaching the Shockley–Queisser limit. Our results highlight the broader potential of designing atomically thin interlayers to enable defect-free incommensurate interfaces.

14 SOLAR ENERGY↗
DOE OSTI2022

Sas20 is a highly flexible starch-binding protein in the Ruminococcus bromii cell-surface amylosome

Ruminococcus bromii is a keystone species in the human gut that has the rare ability to degrade dietary resistant starch (RS). This bacterium secretes a suite of starch-active proteins that work together within larger complexes called amylosomes that allow R. bromii to bind and degrade RS. Starch adherence system protein 20 (Sas20) is one of the more abundant proteins assembled within amylosomes, but little could be predicted about its molecular features based on amino acid sequence. Here, we performed a structure–function analysis of Sas20 and determined that it features two discrete starch-binding domains separated by a flexible linker. We show that Sas20 domain 1 contains an N-terminal β-sandwich followed by a cluster of α-helices, and the nonreducing end of maltooligosaccharides can be captured between these structural features. Furthermore, the crystal structure of a close homolog of Sas20 domain 2 revealed a unique bilobed starch-binding groove that targets the helical α1,4-linked glycan chains found in amorphous regions of amylopectin and crystalline regions of amylose. Affinity PAGE and isothermal titration calorimetry demonstrated that both domains bind maltoheptaose and soluble starch with relatively high affinity (K d ≤ 20 μM) but exhibit limited or no binding to cyclodextrins. Finally, small-angle X-ray scattering analysis of the individual and combined domains support that these structures are highly flexible, which may allow the protein to adopt conformations that enhance its starch-targeting efficiency. Taken together, we conclude that Sas20 binds distinct features within the starch granule, facilitating the ability of R. bromii to hydrolyze dietary RS.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Crystallographic structure and crystal field parameters in the [An IV (DPA) 3 ] 2- series, An = Th, U, Np, Pu

The [An IV (DPA) 3 ] 2- series with An = Th, U, Np, Pu has been synthesized and characterized using SC-XRD and vibrational spectroscopy. First principles calculations were performed, the total electron density is analyzed using the Quantum Theory of Atoms in Molecules. Crystal field parameters and strength parameters are deduced following a previous work on the Ln III analog series e.g. [J. Jung et al., Chem. – Eur. J., 2019, 25, 15112]. The trends in the parameters along the series are compared to the Ln III complexes. They evidence larger covalent interactions and larger J mixing.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Benchmarking machine learning interatomic potentials via phonon anharmonicity

Abstract Machine learning approaches have recently emerged as powerful tools to probe structure-property relationships in crystals and molecules. Specifically, machine learning interatomic potentials (MLIPs) can accurately reproduce first-principles data at a cost similar to that of conventional interatomic potential approaches. While MLIPs have been extensively tested across various classes of materials and molecules, a clear characterization of the anharmonic terms encoded in the MLIPs is lacking. Here, we benchmark popular MLIPs using the anharmonic vibrational Hamiltonian of ThO 2 in the fluorite crystal structure, which was constructed from density functional theory (DFT) using our highly accurate and efficient irreducible derivative methods. The anharmonic Hamiltonian was used to generate molecular dynamics (MD) trajectories, which were used to train three classes of MLIPs: Gaussian approximation potentials, artificial neural networks (ANN), and graph neural networks (GNN). The results were assessed by directly comparing phonons and their interactions, as well as phonon linewidths, phonon lineshifts, and thermal conductivity. The models were also trained on a DFT MD dataset, demonstrating good agreement up to fifth-order for the ANN and GNN. Our analysis demonstrates that MLIPs have great potential for accurately characterizing anharmonicity in materials systems at a fraction of the cost of conventional first principles-based approaches.

interatomic potentials↗
DOE OSTI2021

Thermal fluctuations and carrier localization induced by dynamic disorder in MAPbI 3 described by first-principles based tight-binding model

Halide perovskites are strongly influenced by large amplitude anharmonic lattice fluctuations at room temperature. We develop a tight binding model for dynamically disordered MAPbI$_3$ based on density functional theory (DFT) calculations to calculate electronic structure for finite temperature crystal structures at the length scale of thermal disorder and carrier localization. The model predicts individual Hamiltonian matrix elements and band structures with high accuracy, owing to the inclusion of additional matrix elements and descriptors for non-Coulombic interactions. We apply this model to electronic structure at length and time scales inaccessible to first principles methods, finding an increase in band gap, carrier mass, and the sub-picosecond fluctuations in these quantities with increasing temperature as well as the onset of carrier localization in large supercells induced by thermal disorder at 300 K. Finally, we identify the length scale $L^*= 5$ nm as the onset of localization in the electronic structure, associated with associated with decreasing band edge fluctuations, increasing carrier mass, and Rashba splitting approaching zero.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Structures of RNA phosphotransferase Tpt1 reveal distinct binding modes for an RNA 2′-PO 4 splice junction versus a 5′-PO 4 mononucleotide

Tpt1 is a widely distributed enzyme that removes an internal RNA 2′-phosphate by transfer to NAD + , via a two-step reaction in which: (i) the RNA 2′-PO 4 attacks NAD + to form an RNA-2′-phospho-(ADP-ribose) intermediate and expel nicotinamide; and (ii) the ADP-ribose O2″ attacks the RNA 2′-phosphodiester to form 2′-OH RNA and ADP-ribose-1″,2″-cyclic phosphate products. Tpt1 can also execute a single-step ADP-ribosyltransferase reaction at a 5′-monophosphate nucleic acid terminus that installs a 5′-phospho-ADP-ribose cap structure. Here we present crystal structures of Tpt1 bound to an RNA containing an internal 2′-PO 4 mark (the substrate for the canonical Tpt1 pathway) and in a complex with 5′-AMP. We find that Tpt1 has distinct binding modes, whereby the RNA 2′-PO 4 and the AMP 5′-PO 4 are engaged by the same set of active site amino acids, but the 2′-PO 4 nucleoside and the 5′-nucleoside occupy different sites on the enzyme.

Biochemistry & Molecular Biology↗
DOE OSTI2024

Exploring the fragmentation efficiency of proteins analyzed by MALDI-TOF-TOF tandem mass spectrometry using computational and statistical analyses

Matrix-assisted laser desorption/ionization time-of-flight-time-of-flight (MALDI-TOF-TOF) tandem mass spectrometry (MS/MS) is a rapid technique for identifying intact proteins from unfractionated mixtures by top-down proteomic analysis. MS/MS allows isolation of specific intact protein ions prior to fragmentation, allowing fragment ion attribution to a specific precursor ion. However, the fragmentation efficiency of mature, intact protein ions by MS/MS post-source decay (PSD) varies widely, and the biochemical and structural factors of the protein that contribute to it are poorly understood. With the advent of protein structure prediction algorithms such as Alphafold2, we have wider access to protein structures for which no crystal structure exists. In this work, we use a statistical approach to explore the properties of bacterial proteins that can affect their gas phase dissociation via PSD. We extract various protein properties from Alphafold2 predictions and analyze their effect on fragmentation efficiency. Our results show that the fragmentation efficiency from cleavage of the polypeptide backbone on the C-terminal side of glutamic acid (E) and asparagine (N) residues were nearly equal. In addition, we found that the rearrangement and cleavage on the C-terminal side of aspartic acid (D) residues that result from the aspartic acid effect (AAE) were higher than for E- and N-residues. From residue interaction network analysis, we identified several local centrality measures and discussed their implications regarding the AAE. We also confirmed the selective cleavage of the backbone at D-proline bonds in proteins and further extend it to N-proline bonds. Finally, we note an enhancement of the AAE mechanism when the residue on the C-terminal side of D-, E- and N-residues is glycine. To the best of our knowledge, this is the first report of this phenomenon. Our study demonstrates the value of using statistical analyses of protein sequences and their predicted structures to better understand the fragmentation of the intact protein ions in the gas phase.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Effects of Al Substitution for Fe in Na₅FeSi₄O₁₂ (5.1.8) Glasses: Structure and Crystallization

In this study, the effects of substituting Al for Fe in 5Na2O∙(Al2O3)x∙(Fe2O3)1-x∙8SiO2 glass, x=0 to 1, and Na5AlxFe1-xSi4O12 (5.1.8) crystal, were investigated using thermal analysis, Fe K-edge X-ray absorption, X-ray diffraction, Raman spectroscopy, and Electron Probe Microanalysis. In both glass and crystallized glass, nearly all the Fe was tetrahedrally coordinated Fe3+, as expected from the high concentration of Na2O. The substitution of Al for Fe in the glasses caused the glass transition temperature to increase as polymerization increased, as evidenced by Raman, likely due to both field strength differences of Al vs Fe and a small amount of Fe2+ network modifier present with Fe. After heat treatment at 700 °C for 24 hours, the glasses had crystallized, forming Na2SiO3 and NaAlSiO4 in compositions with high Al concentrations and the 5.1.8 crystal in compositions with high Fe concentrations. Through electron microprobe, it was determined that <0.04 formula unit Al incorporated into the 5.1.8 crystal, i.e. Na5Fe0.96Al0.04Si4O12. The 5.1.8 crystal only formed when Fe concentration was higher than Al in the starting glass.

Antonio, Raine (ORCID:0009000634297975)↗
DOE OSTI2023

Synthesis and physical properties of a new layered ferromagnet Cr 1.21 Te 2

Single crystals of a new layered compound, Cr 1.21 Te 2 , were synthesized via a vapor transport method. The crystal structure and physical properties were characterized by single crystal and powder x-ray diffraction, temperature- and field-dependent magnetization, zero-field heat capacity, and angle-resolved photoemission spectroscopy. Cr 1.21 Te 2 , containing two Cr sites, crystalizes in a trigonal structure with a space group P-3 (No. 147). The Cr site in the interstitial layer is partially occupied. Physical property characterizations indicate that Cr 1.21 Te 2 is metallic with hole pockets at the Fermi energy and undergoes a ferromagnetic phase transition at ~ 173 K. The magnetic moments align along the c axis in the ferromagnetic state. Based on low-temperature magnetization, the spin stiffness constant, D, and spin excitation gap, Δ , were estimated according to Bloch's law to be D = 94 ± 17 meV Å 2 and Δ = 0.45 ± 0.33 meV, suggesting its possible application as a low dimensional ferromagnet.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Sub-molecular structural relaxation at a physisorbed interface with monolayer organic single-crystal semiconductors

Arranging molecules into highly symmetric, topological crystal structures has been recognized as the best approach to functionalize electronic properties in molecular crystals, where the constituent molecules have been assumed to be rigid in shape. Here, in striking contrast, we demonstrate that the molecules in a monolayer organic crystal can undergo a significant deformation in proximity to the substrate, which is reflected by an asymmetry in the electron density profile. X-ray reflectivity and X-ray absorption spectroscopies in conjunction with density-functional theory calculations reveal that the highly planarized π-core are deformed into a bent shape, while the bulk lattice parameters are maintained. The molecular shape change is found to be perfectly suppressed in a bilayer single crystal, which leads to a 40% increase in mobility in the bilayer crystal. Our finding of a unique, sub-molecular scale shape change in monolayer single crystals can offer possibilities for functionalizing electrical properties via nano-scale physisorption.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Structural Asymmetry and Chiral-Induced Spin Selectivity in Chiral Palladium-Halide Semiconductors

Chiral Pb-free metal-halide semiconductors (MHSs) have attracted considerable attention in the field of spintronics due to various interesting spin-related properties and chiral-induced spin selectivity (CISS) effect. Despite their excellent chemical and structural tunability, the material scope and crystal structure of Pb-free chiral MHSs exhibiting the CISS effect are still limited; chiral MHSs that have metal-halide structures of octahedra and tetrahedra are only reported. Here, we report a new class of chiral MHSs, of which palladium (Pd)-halides are formed in 1D square-pyramidal structures or 0D square-planar structures, with a general formula of ((R/S-MBA) 2 PdBr 4 ) 1-x ((R/S-MBA) 2 PdCl 4 ) x (MBA = methylbenzylammonium; x = 0, 0.25, 0.5, 0.75, and 1) for the first time. The crystals adopt the 1D helical chain of Pd-halide square-pyramid (for x = 0, 0.25, 0.5, and 0.75) and 0D structure of Pd-halide square-plane (for x = 1). All the Pd-halides are distorted by the interaction between the halide and the chiral organic ammonium and arranged in a noncentrosymmetric position. Circular dichroism (CD) for ((R/S-MBA) 2 PdBr 4 ) 1-x ((R/S-MBA) 2 PdCl 4 ) x indicates that chirality was transferred from chiral organic ammonium to Pd-halide inorganics. ((R-MBA) 2 PdBr 4 ) 1-x ((R-MBA) 2 PdCl 4 ) x (x = 0, 0.25, 0.5, and 0.75) shows a distortion index of 0.127-0.128, which is the highest value among the previously reported chiral MHSs to the best of our knowledge. We also find that (R/S-MBA) 2 Pd(Br 1-x Cl x ) 4 crystals grow along the out-of-plane direction during spin coating and have high c-axis orientation and crystallinity, and (R/S-MBA) 2 Pd(Br 1-x Cl x ) 4 (x = 0 and 0.5) crystals exhibit a CISS effect in polycrystalline bulk films. In conclusion, these results demonstrate the possibility of a new metal-halide series with square-planar structures or square-pyramidal structures for future spintronic applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗